We evaluate our model on 182 mouse embryonic stem cells transcriptomes measured across 6 thousand genes, where the stage of the cell cycle is determined a priori and provided for each cell[1]}. During training, we provide annotations from 29 hallmark gene sets and 54 reactome gene sets with a median size of 68 genes. As expected, the model robustly identifies biological pathways responsible for the cell cycle. Cell cycle (R), G2/M checkpoint (H) and P53 pathway (H) comprise three of the top five candidates in terms of variance explained.
While both the cell cycle and the G2/M checkpoint factors contribute in finding sub-populations of cells during the same cell cycle phase, the G2/M checkpoint is a stronger indicator of cells in the G2/M phase as supported by their corresponding area under the ROC curve (AUC) of 0.76 and 0.82, respectively.
